Plot point of KOTFE/ET; the Alliance is supposed to be a blend of Light and Dark, Republic and Empire, Jedi and Sith, all working together towards the defeat of Arcann/Vaylin. (Even Satele Shan and the ghost of Darth Marr were in hiding together on Odessan, waiting for the Outlander's arrival...)
Companions: Kira (Child of the Emperor, but rejected him to be a Jedi, despite early training on Korriban), Jaesa (discovered the hypocrisy of parts of the Jedi Order and joined a Sith who she saw as more honest to learn from them, whether it's Light or Dark Jaesa…), Ashara (Jedi Padawan with a special ability who trained under a Sith with the same ability, but didn't necessarily become Sith herself)
Any one of those companions could have had a good quest where you had to recruit them as part of forging the Alliance together, getting Sith and Jedi to find common ground, maybe having to recover training materials from Tython and Korriban through Eternal Empire interdiction as part of it. Could have even included some NPCs discovering that, despite training as Jedi or Sith to start with, they're actually more capable of relating to the Code and ways of the other Order instead... End with Kira/Jaesa/Ashara (or even a combination thereof) thanking the player for helping to preserve the knowledge and teachings the Eternal Empire is trying to destroy and joining/rejoining them.